RNA-seq Analysis Report

Generated by BioInsight AI Pipeline | 2026-01-07 11:22 | Cancer Type: lung_cancer

62
Significant DEGs
10
Hub Genes
17
DB Matched
0
High Confidence
7
Novel Candidates
15
Enriched Pathways

Integrated Gene Analysis

Gene IdLog2FcPadjIs HubDb MatchedConfidenceTags
BRCA1-2.330.0005YesYesmediumHUB_GENE;PATHWAY_CENTRAL
PIK3CA2.080.05YesYesmediumHUB_GENE;PATHWAY_CENTRAL
MYC-2.550.0059YesYesmediumHUB_GENE;PATHWAY_CENTRAL
BRAF-2.380.0029NoYesmediumKNOWN_CANCER_GENE;PATHWAY_CENTRAL
ERBB22.540.02NoYesmediumKNOWN_CANCER_GENE;PATHWAY_CENTRAL
MET-2.710.0076NoYesmediumKNOWN_CANCER_GENE;PATHWAY_CENTRAL
EGFR2.560.0071NoYesmediumKNOWN_CANCER_GENE;PATHWAY_CENTRAL
ROS1-2.800.02NoYesmediumKNOWN_CANCER_GENE;PATHWAY_CENTRAL
ALK2.620.0046NoYesmediumKNOWN_CANCER_GENE;PATHWAY_CENTRAL
KRAS2.380.04NoYesmediumKNOWN_CANCER_GENE;PATHWAY_CENTRAL
PTEN2.150.0065NoYeslowPATHWAY_CENTRAL
RB12.600.02NoYeslowPATHWAY_CENTRAL
BRCA2-1.990.0043NoYeslowPATHWAY_CENTRAL
APC-2.710.0006NoYeslowPATHWAY_CENTRAL
CDK4-1.940.05NoYeslowPATHWAY_CENTRAL
CDKN2A1.790.0022NoYeslowPATHWAY_CENTRAL
TP532.170.0016NoYeslowPATHWAY_CENTRAL
GENE321.070.03YesNonovel_candidateNOVEL_CANDIDATE;HUB_GENE
GENE481.490.0035YesNonovel_candidateNOVEL_CANDIDATE;HUB_GENE
GENE18-1.910.02YesNonovel_candidateNOVEL_CANDIDATE;HUB_GENE
GENE301.760.0082YesNonovel_candidateNOVEL_CANDIDATE;HUB_GENE
GENE101.290.04YesNonovel_candidateNOVEL_CANDIDATE;HUB_GENE
GENE311.580.0057YesNonovel_candidateNOVEL_CANDIDATE;HUB_GENE
GENE551.450.0071YesNonovel_candidateNOVEL_CANDIDATE;HUB_GENE
VEGFA-1.460.0076NoNorequires_validationTME_SIGNAL;PATHWAY_CENTRAL;REQUIRES_VALIDATION
GENE451.350.04NoNorequires_validationREQUIRES_VALIDATION
GENE151.380.02NoNorequires_validationREQUIRES_VALIDATION
GENE21-1.930.02NoNorequires_validationREQUIRES_VALIDATION
GENE20-1.130.02NoNorequires_validationREQUIRES_VALIDATION
GENE171.380.04NoNorequires_validationREQUIRES_VALIDATION
GENE54-1.460.05NoNorequires_validationREQUIRES_VALIDATION
GENE441.500.02NoNorequires_validationREQUIRES_VALIDATION
GENE332.020.03NoNorequires_validationREQUIRES_VALIDATION
GENE35-1.740.04NoNorequires_validationREQUIRES_VALIDATION
GENE39-1.150.02NoNorequires_validationREQUIRES_VALIDATION
GENE22-1.340.03NoNorequires_validationREQUIRES_VALIDATION
GENE141.450.03NoNorequires_validationREQUIRES_VALIDATION
GENE41-1.420.02NoNorequires_validationREQUIRES_VALIDATION
GENE11-1.430.0076NoNorequires_validationREQUIRES_VALIDATION
GENE13-1.280.02NoNorequires_validationREQUIRES_VALIDATION
GENE561.380.0031NoNorequires_validationREQUIRES_VALIDATION
GENE251.620.0006NoNorequires_validationREQUIRES_VALIDATION
GENE531.700.0012NoNorequires_validationREQUIRES_VALIDATION
GENE401.330.0016NoNorequires_validationREQUIRES_VALIDATION
GENE42-1.560.0016NoNorequires_validationREQUIRES_VALIDATION
GENE471.460.0016NoNorequires_validationREQUIRES_VALIDATION
GENE501.460.0025NoNorequires_validationREQUIRES_VALIDATION
GENE511.820.0026NoNorequires_validationREQUIRES_VALIDATION
CTLA42.140.0029NoNorequires_validationTME_SIGNAL;REQUIRES_VALIDATION
GENE24-1.670.0029NoNorequires_validationREQUIRES_VALIDATION
GENE43-1.310.0033NoNorequires_validationREQUIRES_VALIDATION
GENE26-1.220.02NoNorequires_validationREQUIRES_VALIDATION
GENE58-1.820.0043NoNorequires_validationREQUIRES_VALIDATION
GENE231.810.0043NoNorequires_validationREQUIRES_VALIDATION
GENE271.660.0057NoNorequires_validationREQUIRES_VALIDATION
GENE161.680.0059NoNorequires_validationREQUIRES_VALIDATION
GENE59-1.380.0064NoNorequires_validationREQUIRES_VALIDATION
GENE121.270.0006NoNorequires_validationREQUIRES_VALIDATION
GENE38-1.360.0076NoNorequires_validationREQUIRES_VALIDATION
GENE342.310.01NoNorequires_validationREQUIRES_VALIDATION
CD2742.160.01NoNorequires_validationTME_SIGNAL;REQUIRES_VALIDATION
GENE49-1.350.05NoNorequires_validationREQUIRES_VALIDATION

Interpretation Results

Interpretation Guidelines Applied

  • DEG alone does not equal biological importance
  • DB match provides context, not proof
  • DB mismatch means unknown, not unimportant
  • Hub status increases confidence for novel candidates
  • Pathway context strengthens interpretation

DB-Matched Genes

BRCA1

Confidence: medium

BRCA1 shows significant downregulated expression (log2FC=-2.33, padj<0.05). While BRCA1 is catalogued in cancer databases, it is not specifically associated with lung_cancer. Its role in this cancer type may warrant further investigation. Pathway analysis places BRCA1 in 17 enriched pathway(s), providing functional context for its potential role.

Tags: HUB_GENE, PATHWAY_CENTRAL

MYC

Confidence: medium

MYC shows significant downregulated expression (log2FC=-2.55, padj<0.05). While MYC is catalogued in cancer databases, it is not specifically associated with lung_cancer. Its role in this cancer type may warrant further investigation. Pathway analysis places MYC in 55 enriched pathway(s), providing functional context for its potential role.

Tags: HUB_GENE, PATHWAY_CENTRAL

PIK3CA

Confidence: medium

PIK3CA shows significant upregulated expression (log2FC=2.08, padj<0.05). While PIK3CA is catalogued in cancer databases, it is not specifically associated with lung_cancer. Its role in this cancer type may warrant further investigation. Pathway analysis places PIK3CA in 69 enriched pathway(s), providing functional context for its potential role.

Tags: HUB_GENE, PATHWAY_CENTRAL

BRAF

Confidence: medium

BRAF shows significant downregulated expression (log2FC=-2.38, padj<0.05). This gene is a known cancer gene specifically associated with lung_cancer, supporting its biological relevance in this context. Pathway analysis places BRAF in 47 enriched pathway(s), providing functional context for its potential role.

Tags: KNOWN_CANCER_GENE, PATHWAY_CENTRAL

ALK

Confidence: medium

ALK shows significant upregulated expression (log2FC=2.62, padj<0.05). This gene is a known cancer gene specifically associated with lung_cancer, supporting its biological relevance in this context. Pathway analysis places ALK in 16 enriched pathway(s), providing functional context for its potential role.

Tags: KNOWN_CANCER_GENE, PATHWAY_CENTRAL

EGFR

Confidence: medium

EGFR shows significant upregulated expression (log2FC=2.56, padj<0.05). This gene is a known cancer gene specifically associated with lung_cancer, supporting its biological relevance in this context. Pathway analysis places EGFR in 82 enriched pathway(s), providing functional context for its potential role.

Tags: KNOWN_CANCER_GENE, PATHWAY_CENTRAL

MET

Confidence: medium

MET shows significant downregulated expression (log2FC=-2.71, padj<0.05). This gene is a known cancer gene specifically associated with lung_cancer, supporting its biological relevance in this context. Pathway analysis places MET in 31 enriched pathway(s), providing functional context for its potential role.

Tags: KNOWN_CANCER_GENE, PATHWAY_CENTRAL

ERBB2

Confidence: medium

ERBB2 shows significant upregulated expression (log2FC=2.54, padj<0.05). This gene is a known cancer gene specifically associated with lung_cancer, supporting its biological relevance in this context. Pathway analysis places ERBB2 in 52 enriched pathway(s), providing functional context for its potential role.

Tags: KNOWN_CANCER_GENE, PATHWAY_CENTRAL

ROS1

Confidence: medium

ROS1 shows significant downregulated expression (log2FC=-2.80, padj<0.05). This gene is a known cancer gene specifically associated with lung_cancer, supporting its biological relevance in this context. Pathway analysis places ROS1 in 14 enriched pathway(s), providing functional context for its potential role.

Tags: KNOWN_CANCER_GENE, PATHWAY_CENTRAL

KRAS

Confidence: medium

KRAS shows significant upregulated expression (log2FC=2.38, padj<0.05). This gene is a known cancer gene specifically associated with lung_cancer, supporting its biological relevance in this context. Pathway analysis places KRAS in 70 enriched pathway(s), providing functional context for its potential role.

Tags: KNOWN_CANCER_GENE, PATHWAY_CENTRAL

Novel Candidates

GENE48

Hypothesis: potential novel regulator

GENE48 shows significant upregulated expression (log2FC=1.49, padj<0.05). Although not in major cancer databases, GENE48 emerged as a hub gene (degree=1), suggesting potential regulatory importance. This may represent a novel candidate for this cancer type.

GENE31

Hypothesis: potential novel regulator

GENE31 shows significant upregulated expression (log2FC=1.58, padj<0.05). Although not in major cancer databases, GENE31 emerged as a hub gene (degree=1), suggesting potential regulatory importance. This may represent a novel candidate for this cancer type.

GENE55

Hypothesis: potential novel regulator

GENE55 shows significant upregulated expression (log2FC=1.45, padj<0.05). Although not in major cancer databases, GENE55 emerged as a hub gene (degree=1), suggesting potential regulatory importance. This may represent a novel candidate for this cancer type.

GENE30

Hypothesis: potential novel regulator

GENE30 shows significant upregulated expression (log2FC=1.76, padj<0.05). Although not in major cancer databases, GENE30 emerged as a hub gene (degree=1), suggesting potential regulatory importance. This may represent a novel candidate for this cancer type.

GENE18

Hypothesis: potential novel regulator

GENE18 shows significant downregulated expression (log2FC=-1.91, padj<0.05). Although not in major cancer databases, GENE18 emerged as a hub gene (degree=1), suggesting potential regulatory importance. This may represent a novel candidate for this cancer type.

GENE32

Hypothesis: potential novel regulator

GENE32 shows significant upregulated expression (log2FC=1.07, padj<0.05). Although not in major cancer databases, GENE32 emerged as a hub gene (degree=1), suggesting potential regulatory importance. This may represent a novel candidate for this cancer type.

GENE10

Hypothesis: potential novel regulator

GENE10 shows significant upregulated expression (log2FC=1.29, padj<0.05). Although not in major cancer databases, GENE10 emerged as a hub gene (degree=1), suggesting potential regulatory importance. This may represent a novel candidate for this cancer type.

VEGFA

Hypothesis: TME signal

VEGFA shows significant downregulated expression (log2FC=-1.46, padj<0.05). VEGFA is associated with tumor microenvironment signaling. Its expression change may reflect stromal or immune cell activity rather than tumor-intrinsic changes. Pathway analysis places VEGFA in 47 enriched pathway(s), providing functional context for its potential role.

GENE12

Hypothesis: requires functional validation

GENE12 shows significant upregulated expression (log2FC=1.27, padj<0.05). GENE12 is not catalogued in major cancer databases. Its significance remains to be determined through functional validation.

GENE25

Hypothesis: requires functional validation

GENE25 shows significant upregulated expression (log2FC=1.62, padj<0.05). GENE25 is not catalogued in major cancer databases. Its significance remains to be determined through functional validation.

Pathway Enrichment

DatabaseTerm NamePadjGene Count
KEGG_2021_HumanBladder cancer0.000010
KEGG_2021_HumanNon-small cell lung cancer0.000011
KEGG_2021_HumanPancreatic cancer0.000011
KEGG_2021_HumanBreast cancer0.000013
KEGG_2021_HumanMelanoma0.000010
GO_Molecular_Function_2023Transmembrane Receptor Protein Kinase Activity (GO:0019199)0.00054
GO_Molecular_Function_2023Protein Tyrosine Kinase Activity (GO:0004713)0.00065
GO_Molecular_Function_2023Transmembrane Receptor Protein Tyrosine Kinase Activity (GO:0004714)0.00064
GO_Biological_Process_2023Positive Regulation Of Transferase Activity (GO:0051347)0.00116
GO_Biological_Process_2023Regulation Of Cell Growth (GO:0001558)0.00117
GO_Biological_Process_2023Regulation Of Kinase Activity (GO:0043549)0.00115
GO_Biological_Process_2023Negative Regulation Of Cell Cycle (GO:0045786)0.00115
GO_Biological_Process_2023Positive Regulation Of Phosphorylation (GO:0042327)0.00117
GO_Molecular_Function_2023Protein Phosphatase Binding (GO:0019903)0.014
GO_Molecular_Function_2023Ubiquitin Protein Ligase Binding (GO:0031625)0.035

Visualizations

Network Graph

Network Graph

Volcano Plot

Volcano Plot

Interpretation Summary

Interpretation Summary

Pca Plot

Pca Plot

Pathway Barplot

Pathway Barplot

Heatmap Top50

Heatmap Top50

Methods

Analysis Pipeline

  • DEG Analysis: DESeq2 with |log2FC| > 1, padj < 0.05
  • Network Analysis: NetworkX co-expression network, Spearman correlation > 0.7
  • Pathway Enrichment: gseapy with GO (BP, MF, CC) and KEGG databases
  • DB Validation: COSMIC Tier 1, OncoKB gene matching
  • Interpretation: Systematic checklist-based scoring

Confidence Scoring

  • Hub gene: +2 points
  • DB matched: +2 points
  • Cancer type specific: +1.5 points
  • High pathway involvement: +0.5 points

Confidence Thresholds

  • High: Score ≥ 5 and DB matched
  • Medium: Score ≥ 3 and DB matched
  • Novel Candidate: Not in DB but is Hub gene
  • Requires Validation: Score < 1.5